Hi, Steve,

thanks.
Is there no other possibiliy? Like setting a search option that non-ring should not match ring atoms? The reason I am asking is that my query molecules come from an SD file, so converting them into Smarts would be difficult.

Kind regards,
Axel


On 29.06.2018 10:06, Stephen Roughley wrote:
Axel,

You need to use a SMARTS query:

q = Chem.MolFromSmarts("[CR0][CR0][CR0]")

Have a look at http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

Steve

On 29 June 2018 at 08:04, Axel Pahl <axelp...@gmx.de <mailto:axelp...@gmx.de>> wrote:

    Dear all,

    my google-fu is failing is me.
    Is it possible in substructure searches to have chain atoms NOT
    match ring atoms?

    In essence, I would like the following example query for n-propane
    in cyclo-hexane to return False (currently it is returning True):

    mol = Chem.MolFromSmiles("C1CCCCC1")
    q = Chem.MolFromSmiles("CCC")
    print(mol.HasSubstructMatch(q))  # ==> True

    Many thanks in advance for your help.

    Kind regards,
    Axel

    
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